Egyptian women cast their votes in the presidential runoff at a polling station in Cairo. Photograph: Majdi Fathi/ Majdi Fathi/ZUMA Press/Corbis

A few young Egyptians are sitting innocently in a cafe when an ominous, English-speaking stranger appears at the door. Instinctively, they invite him to join them and waste no time bemoaning the state of the nation – complaining of high prices, petrol shortages, and a dastardly plot against the military that is being hatched on the underground network. Little do they realise the foreigner's real intention: to text all of this information to his western spy handler.

This was the scene that played out on Egyptian state television this week, not as part of a James Bond rip-off, but as a government-sponsored advertisement, replete with doom-laden music, warning citizens not to talk to foreigners armed with tweet-ready smart phones.

The 30-second commercial has provoked a barrage of spoofs, but beyond the mockery it is also a window on to the increasingly toxic political mood that has engulfed Egypt since the toppling of dictator Hosni Mubarak in February 2011, and reached frightening levels as this weekend's presidential runoff vote takes place. The choice is between Mubarak's last premier and air-force commander Ahmed Shafiq, and the Muslim Brotherhood's second choice pick Mohamed Morsi. For many disillusioned voters it is hardly a choice at all.

"The revolution was stolen from us," merchant Nabil Abdel-Fatah told reporters as he queued outside a polling centre in Cairo's working-class district of Imbaba. He said he planned to vote for Shafiq. "We can easily get rid of him if we want to, but not the Brotherhood, which will cling to power."

Outside the same polling centre in Imbaba, which is a stronghold for Islamists, Amin Sayed said: "If Shafiq wins, we will return to the street."

The botched "transitional" period overseen by the junta, the supreme council of the armed forces (Scaf), has polarised society. Since the first round result, when several of the pro-revolutionary centre-ground candidates were knocked out, Shafiq and the Brotherhood have exchanged volleys of vitriol.

Shafiq has been the muckraker, egged on by those who harbour deep-rooted fears of potential Islamic rule. He has stated that a Brotherhood presidency will aim to transfer Egypt's capital to Jerusalem, comments that are parroted verbatim by his supporters in the state media. For his part, Morsi is warning that a Shafiq victory would complete the counter-revolution, and restore the Mubarak regime in all its corrupt glory.

Egyptian voters who see one candidate as a representative of the ancient regime and the other as dangerously Islamist are having to hold their nose, or in one case shed blood. Voting for expat Egyptians has already closed: one voter made a tiny cut on his wrist, using his blood to write "Glory to the martyrs" as a third option on the ballot paper.

"We got tricked, but that's because we dared to dream," says 25-year-old primary school teacher Kismet El Husseiny. She is one of many in the centre who voted for another candidate and didn't envisage what was being described as the nightmare scenario even before the first round took place. "I will now boycott, I can't have this on my conscience."

Out of the 23 million voters in the first round of elections last month, 12 million did not vote for either of the runoff candidates. The eventual winner may stumble to the presidency with a mandate from a mere 10% of the electorate.

"Accepting a so-called democratic transition under military rule was a serious error of judgment on the part of civilian revolutionary forces," says writer and commentator Ahmad Shokr, "Today we're paying the price for a deeply flawed process that was intended from the start to safeguard the prerogatives of the ruling military council, not to facilitate a genuine transition to civilian democracy."

Mohamed Abdel-Fatah Ali is a driver from the sprawling working-class suburb of Ain Shams. He is not enthused by his options. "The Brotherhood are liars and cheats. We have Christians, so we need a civil state, not an Islamic one. As for Shafiq, he is the Mubarak sequel, a military man. Why should my elderly parents stand in the sun to vote in this?"

The Brotherhood is also a concern for Egyptian women, with their stance on women's rights vague and ambiguous. Tanya El Kashef, an assistant editor at a city lifestyle website, said: "It's already difficult living in a country that barely accepts females as it is, so to bring in someone who officially believes and advocates that women are a lesser gender is my first concern."

Husseiny says: "When a female Brotherhood MP says there is no sexual harassment in Egypt and women should behave better, this is an insult to me as a woman. You feel sorry for yourself that after all this you're stuck with a choice between Shafiq and Morsi. Some people have sacrificed a lot and it's awful that someone from that system could come back."

When Scaf assumed power from Mubarak last year, it was on a wave of optimism and popularity that would be eroded with every passing setback. Dozens of protesters died and the litany of catastrophes rolled on, most notoriously last October when the military mowed down Coptic Christian demonstrators in downtown Cairo. Thousands of civilians have been subjected to military trials and imprisonment, more than under the three decades of Mubarak rule.

The independence of the judiciary has also come under scrutiny in the wake of a stream of seemingly politicised verdicts, most seriously last Thursday when the supreme constitutional court (SCC) decreed the dissolution of parliament, in which the Muslim Brotherhood was the majority bloc. A day before the SCC rulings, the justice ministry passed a decree granting powers to military police and intelligence operatives to arrest and detain civilians, skirting very closely to the margins of martial law.

"Scaf are the reason for this mess," says Ali. "They are creating a soap opera, an illusion of democracy and what they really want they make happen." Kashef says: "I think the US-funded army picked out their president a while ago and we're just playing along."

A boycott-the-vote movement has sprung from the chaos of the transitional period. Rami Ghanem is a founder of one of the groups. "We are in a very bad situation and it's the worst possible scenario we can envisage," he says. "This is the success of the counter-revolution and the control of Scaf. Islamist politicians deserted the revolution and chased seats. Our only way out is to return to the revolution, including the Islamists. If they don't do it now, we'll all end up in jail, and they'll be the first."

Irrespective of the victor, this climate of divisive mistrust is expected to continue, where each side will paint the other as the mindless proxy of a foreign saboteur, with the Egyptians that dared to dream of something different lost in the morass of a transition gone awry.